![]() * Optimization of arbitrary components of the model using a range of diverse algorithms.* Stoichiometric analysis of the reaction network, including mass conservation analysis and elementary flux modes.Models can be analyzed and modified with a large set of methods: Simulations can be of time courses or steady states. * Hybrid LSODA/SSA for hybrid simulations with stochastic kinetics and differential equations.* Hybrid Runge-Kutta/SSA for hybrid simulations with stochastic kinetics and differential equations.* Adaptive SSA/τ-leap algorithm for faster (approximate) stochastic kinetics.* τ-leap algorithm for faster (approximate) stochastic kinetics.* Gibson-Brooke's version of Gillespie's algorithm for exact stochastic kinetics.* Gillespie's direct method for exact stochastic kinetics.* LSODAR for ordinary differential equation modeling.The software provides an interface to create parameter scans (sweeps), parameter sampling and repeated simulations - including complex simulation scenarios mixing parameter samples with scans and repeats of simulations (or other analyses). Simulation can be performed either with stochastic kinetics or with differential equations, and the software easily allows switching between them. Models can also be exported in XPP format, Berkeley Madonna format, and as C code (in addition to MathML and Latex). * the full set of differential equations these can be exported in Latex or MathML formats.ĬOPASI can import and export models in the SBML format (levels 1 to 3).* an arbitrary number of network diagrams (including an SBGN-compliant option).* the GUI interface, with tables for reactions, species, compartments, etc.* The rates of reaction can be picked from a set of predefined kinetic functions (the most common in biochemistry), or arbitrary functions defined by the user.* Compartments can have variable sizes (ie they can be variables of the model). ![]()
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